Identification of QTLs associated with the anaerobic germination potential using a set of Oryza nivara introgression lines

Liu, Licheng; Li, Xiaoxiang; Liu, Sanxiong; Jiang, Min; Liu, Wenqiang; Pan, Xi; Fang, Baohua; Hu, Min; Liu, Zhongqi; Li, Yongchao; Zhang, Haiqing

doi:10.1007/s13258-021-01063-6

Cited by 6 publications

(10 citation statements)

References 41 publications

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“…Based on the high‐density genetic map of the O. nivara introgression lines (IL) population, Liu et al (2021) identified one coleoptile length‐related QTLs ( qCLN1 ) in chromosome 1 under anaerobic conditions. The peak marker (bin150) of qCLN1 was located between 38,174,447 and 38,387,308 bp harboring the “green evolution” gene semi‐dwarf1 ( sd1 ).…”

Section: Discussionmentioning

confidence: 99%

Combination of quantitative trait locus (QTL) mapping and transcriptome analysis reveals submerged germination QTLs and candidate genes controlling coleoptile length in rice

Kong

Zhang

et al. 2021

Food and Energy Security

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Submerged germination ability is a key trait of rice (Oryza sativa L.) in the success of water direct seeding. Therefore, mining submerged germination‐related loci and seeking high tolerant rice germplasms are important for developing rice direct seeding breeding strategies. Here, we treated 272 recombinant inbred lines (RILs, F15) from a cross from Luohui 9 (indica) and RPY geng (japonica) with simulated submergence for 7 days. We successfully bred several superior homozygous RILs with high submergence resistance, namely, R53, R137, R148, R176, and R180, via indica and japonica hybridization strategies. Then, the QTL mapping of coleoptile length trait was performed by R/qtl and IciMapping softwares based on the high‐density bin marker genetic map and two QTLs responsible for coleoptile length were detected in chromosomes 1 (qCL‐1.1) and 3 (qCL‐3.1). The haplotype results of RILs showed that the aggregation of elite alleles of these two QTLs in an individual was beneficial to improving the rice submergence tolerance. According to contrasting genotype of qCL‐1.1 and qCL‐3.1 with different coleoptile lengths, RIL07 (R07) and R180 were selected to further RNA‐seq analysis for analyzing the possible molecular mechanisms of rice under submergence stress. Finally, LOC_Os01g04430, LOC_Os01g04530, and LOC_Os03g22720 for qCL‐1.1 and qCL‐3.1 were characterized to affect submergence stress by the overlapped analysis of two independent sets of RNA‐seq data, qRT‐PCR verification, and gene sequence alignments. In this study, the submerged germination‐related QTLs/genes and high submergence‐tolerant RILs provided new genetic resources for breeding rice varieties suitable for direct seeding via molecular breeding strategies in the immediate future.

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Section: Discussionmentioning

confidence: 99%

Combination of quantitative trait locus (QTL) mapping and transcriptome analysis reveals submerged germination QTLs and candidate genes controlling coleoptile length in rice

Kong

Zhang

et al. 2021

Food and Energy Security

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“…Additional submergence-tolerant alleles ( SUB1A-1 ) were identified from wild rice species O. nivara and O. rufipogon , together with a likely presence of other submergence mechanisms in other wild rice accessions ( Niroula et al, 2012 ). Two anaerobic germination QTLs ( qAGP1 and qAGP3 ) from O. nivara introgression lines ( Liu et al, 2021a ) potentially can be used to enhance flooding tolerance in elite SUB1 genotypes, which are not always tolerant to anaerobic conditions during germination. Wild species with tolerance to waterlogging/stagnant flooding have been reported to possess unique alleles for aerenchyma formation ( Zhang et al, 2017 ), or to provide a stronger barrier to radial oxygen loss ( Pedersen et al, 2021 ).…”

Section: Can We Develop Climate-resilient Crops?mentioning

confidence: 99%

Climate change challenges, plant science solutions

et al. 2022

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Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g., heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.

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“…The location of qCV1-2 overlaps with the physical The distribution of four coleoptile phenotype traits in the RIL population. interval of which qAGP1 (Liu et al, 2021). QCL4-2/qCV4-2 and qCV8-2 are in the same physical regions as qSFW-4 and qRD-8, respectively (Yang et al, 2021).…”

Section: Identification Of Ag-associated Qtlsmentioning

confidence: 99%

“…The tolerance of rice seedlings to hypoxia stress during germination is a complex quantitative trait controlled by multiple gene loci. In previous studies, various genetic populations have been used for linkage and association mapping to identify many QTLs related to seed germination and early seedling tolerance to hypoxia stress (Angaji, 2008;Angaji et al, 2010;Septiningsih et al, 2013;Baltazar et al, 2014;Hsu and Tung, 2015;Baltazar et al, 2019;Yang et al, 2019;Ignacio et al, 2021;Liu et al, 2021). Using the Kinmaze/DV85 recombinant inbred line population, Jiang et al identified five QTLs on chromosomes 1, 2, 5 and 7, respectively, which could explain 10.5% -19.6% of the phenotypic variation.…”

Section: Introductionmentioning

confidence: 99%

“…One QTL, qAGP1 and qAGP3 were detected on chromosomes 1 and 3, which could explain 15% of the phenotypic variation. These two QTLs improved hypoxia tolerance by increasing coleoptile length during rice germination (Liu et al, 2021). Although many QTLs related to hypoxia tolerance in germination have been identified, only a few use substitution lines or near-isogenic lines to evaluate their effects on rice seedling growth, and the molecular mechanism of anaerobic tolerance needs further study.…”

Section: Introductionmentioning

confidence: 99%

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High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice

Liang

Du²,

Pang³

et al. 2022

Front. Plant Sci.

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The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.

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Identification of QTLs associated with the anaerobic germination potential using a set of Oryza nivara introgression lines

Cited by 6 publications

References 41 publications

Combination of quantitative trait locus (QTL) mapping and transcriptome analysis reveals submerged germination QTLs and candidate genes controlling coleoptile length in rice

Combination of quantitative trait locus (QTL) mapping and transcriptome analysis reveals submerged germination QTLs and candidate genes controlling coleoptile length in rice

Climate change challenges, plant science solutions

High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice

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